split genes in different scaffold or the same scaffold

Question

[qwzhang0601]

We are annotating a new genome. We have predict gene models using Maker2. But since there must be split genes within the predicted gene models, we wonder what's the common way to detect such split genes and how to merge them? We have RNA-seq data from the same species and protein sequences from related species. Is there any popular tools to do this?

Thanks

Best Quanwei